The treatment, which will be called Brisdelle, was developed by Noven Pharmaceuticals and consists of a low dose of paroxetine, which is used at higher doses in the antidepressant Paxil.

Approved treatments for menopausal hot flashes until now have all contained the hormone estrogen, sometimes in combination with progestin. But hormone use has decreased sharply since a study in 2002 suggested that the combination of estrogen and progestin could increase the risk of cardiovascular problems and cancer.

“There are a significant number of women who suffer from hot flashes associated with menopause and who cannot or do not want to use hormonal treatments,” Dr. Hylton V. Joffe, director of the F.D.A’s division of bone, reproductive and urologic products, said in a statement.

While the F.D.A. does not have to follow the recommendations of its advisory panels, it is highly unusual for it to approve a drug that receives a strong negative vote. Committee members who voted against it said while there was a need for a nonhormonal therapy, Noven’s candidate was only minimally effective.

The agency did not explain why it went against the panel’s recommendation, saying only that it viewed Brisdelle as a useful treatment that had met its goals in clinical trials.

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Women in the clinical trials for Brisdelle started out with a median of about 10 hot flash episodes a day. After 12 weeks, those who took the drug had a median of nearly six fewer episodes a day, compared with a reduction of four or five episodes a day for those receiving the placebo.

While the difference was statistically significant, many members of the advisory committee said such a difference would not be meaningful to women.

Noven, which is based in Miami and is a subsidiary of Hisamitsu Pharmaceutical of Japan, said Brisdelle would be available in November. It did not say how much the drug would cost.

Dr. Joel Lippman, chief medical officer of Noven, said in a statement that 24 million women in the United States had moderate to severe hot flashes and that two-thirds of them were not currently treating them.

Brisdelle’s label has a strong warning that the drug can increase suicidal thoughts or behavior, language similar to that on the labels of other drugs containing paroxetine. Other warnings include an increased risk of bleeding, and possible reduction in the effectiveness of the breast cancer drug tamoxifen if both drugs are used together.

The advisory panel in March gave an even stronger no vote to another proposed nonhormonal treatment for hot flashes, an extended-release version of the neurology drug gabapentin. In that case, the F.D.A. went along with the panel, rejecting the drug, according to an announcement by its developer, Depomed.

A version of this article appears in print on June 29, 2013, on Page B3 of the New York edition with the headline: Rejecting Advisory Panel’s Finding, F.D.A. Approves a Drug for Hot Flashes. Order Reprints|Today's Paper|Subscribe